Regulatory roles of the epitranscriptome and RNA structurome during vertebrate development

项目总结/摘要 在所有动物中，母体到合子的转变允许单个合子所需的信息转移到 发育成成熟的有机体。受精后，母体程序，由母体遗传的 mRNA和蛋白质驱动细胞发育，并被合子程序取代。因为这 虽然这种转变主要发生在转录沉默的胚胎中，但它在很大程度上依赖于转录后调节。 如果不能正确调节母系遗传的mRNA，通常会导致发育停滞， 异常最近的研究表明，母体mRNA被RNA修饰修饰， 统称为“表转录组”，与不同的mRNA命运相关。此外，我们和其他 在母体到合子过渡期间进行mRNA结构动态的全球分析，并确定 在这一基本过程中，许多地区在结构上发生了变化，其中许多影响了 mRNA衰变。这些研究表明，RNA修饰和动态RNA结构正在出现， 在母体到合子过渡期间基因表达的关键调节因子。然而， 表位转录组和动态RNA结构，以及它们在母体到母体的基因调控中的作用。 合子转换仍然知之甚少。此外，RNA修饰和结构相互影响 调节RNA功能，但很少有人知道它们如何相互作用，以控制基因表达， 脊椎动物发育我实验室的主要目标是了解表转录组和RNA 结构介导的基因调控网络，单独和合作，在脊椎动物的发展， 他们的功能障碍如何促进发育缺陷或疾病。在这里，我们假设RNA 修饰和结构与反式因子相互作用，参与转录后调控， 景观驱动脊椎动物的发展。为了验证这一假设，我们将联合收割机斑马鱼-一种体内 脊椎动物发展的模式-及其创新的多组学方法的遗传工具箱。来 在接下来的五年里，我们将检查天然转录组，以生成全球性的，但详细的， 在母体到合子过渡期间的表位转录组，并研究特定的RNA修饰如何影响 基因表达。我们还将破译由转录组的动态区域形成的RNA折叠， 分析它们对RNA调控的影响。我们将确定与RNA修饰相互作用的反式因子， 感兴趣的结构，并研究其功能丧失对基因表达和脊椎动物 发展最后，我们将研究RNA修饰和结构如何合作调节后， 转录调控这些调查的成功完成将大大增加现有的 RNA修饰和结构如何协调转录后调控的知识，并将 扩大我们对脊椎动物发育的分子机制的理解。

PROJECT SUMMARY/ABSTRACT In all animals, the maternal-to-zygotic transition allows the transfer of information required for a single zygote to develop into a mature organism. After fertilization, the maternal program, composed of maternally-inherited mRNAs and proteins, drives cellular development and is replaced by the zygotic program. Because this transition occurs primarily in a transcriptionally silent embryo, it relies heavily on post-transcriptional regulation. Failure to properly regulate maternally-inherited mRNAs generally leads to developmental arrest or abnormalities. Recent studies have shown that maternal mRNAs are decorated with RNA modifications, collectively known as the ‘epitranscriptome’, that correlate with different mRNA fates. Moreover, we and others performed global analyses of mRNA structure dynamics during the maternal-to-zygotic transition and identified numerous regions that are structurally remodeled during this fundamental process, many of which impact mRNA decay. These studies suggest that RNA modifications and dynamic RNA structures are emerging as key regulators of gene expression during the maternal-to-zygotic transition. However, the detailed landscape of the epitranscriptome and dynamic RNA structures, and their roles in gene regulation during the maternal-to- zygotic transition remain poorly understood. Furthermore, RNA modifications and structures affect one another to regulate RNA functions, but little is known about how they interact to control gene expression during vertebrate development. The primary goal of my lab is to understand how the epitranscriptome and RNA structures mediate gene regulatory networks, separately and cooperatively, during vertebrate development and how their dysfunction promotes developmental defects or diseases. Here, we hypothesize that RNA modifications and structures interact with trans-factors to participate in the post-transcriptional regulatory landscape driving vertebrate development. To test this hypothesis, we will combine zebrafish —an in vivo model of vertebrate development— and its genetic toolbox with innovative multi-omics approaches. Over the next five years, we will inspect the native transcriptome to generate global, yet detailed, maps of the epitranscriptome during the maternal-to-zygotic transition, and study how specific RNA modifications impact gene expression. We will also decipher the RNA folds formed by dynamic regions of the transcriptome and analyze their effect on RNA regulation. We will identify trans-factors interacting with RNA modifications and structures of interest and study the consequences of their loss-of-function on gene expression and vertebrate development. Finally, we will examine how RNA modifications and structures cooperate to modulate post- transcriptional regulation. Successful completion of these investigations will greatly increase the existing knowledge of how RNA modifications and structures orchestrate post-transcriptional regulation, and will expand our understanding of the molecular mechanisms shaping vertebrate development.